Correlation between copy number variation genes (focal events) and selected clinical features
Glioblastoma Multiforme (Primary solid tumor)
15 July 2014  |  analyses__2014_07_15
Maintainer Information
Citation Information
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variation genes (focal events) and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1WM1C42
Overview
Introduction

This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.

Summary

Testing the association between copy number variation 71 focal events and 8 clinical features across 560 patients, 16 significant findings detected with Q value < 0.25.

  • amp_7p11.2 cnv correlated to 'Time to Death' and 'AGE'.

  • amp_7q11.21 cnv correlated to 'Time to Death' and 'AGE'.

  • amp_7q21.2 cnv correlated to 'Time to Death' and 'AGE'.

  • del_9p21.3 cnv correlated to 'AGE'.

  • del_10p15.3 cnv correlated to 'Time to Death' and 'AGE'.

  • del_10p13 cnv correlated to 'Time to Death' and 'AGE'.

  • del_10p11.23 cnv correlated to 'Time to Death' and 'AGE'.

  • del_10q23.31 cnv correlated to 'Time to Death' and 'AGE'.

  • del_10q26.3 cnv correlated to 'AGE'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 71 focal events and 8 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 16 significant findings detected.

Clinical
Features
Time
to
Death
AGE GENDER KARNOFSKY
PERFORMANCE
SCORE
HISTOLOGICAL
TYPE
RADIATIONS
RADIATION
REGIMENINDICATION
RACE ETHNICITY
nCNV (%) nWild-Type logrank test Wilcoxon-test Fisher's exact test Wilcoxon-test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
amp 7p11 2 492 (88%) 68 4.09e-07
(0.00023)
6.33e-12
(3.6e-09)
0.427
(1.00)
0.104
(1.00)
0.0566
(1.00)
0.0716
(1.00)
0.476
(1.00)
0.0584
(1.00)
amp 7q11 21 450 (80%) 110 3.31e-05
(0.0184)
3.29e-07
(0.000185)
0.327
(1.00)
0.619
(1.00)
0.00675
(1.00)
0.137
(1.00)
0.264
(1.00)
0.14
(1.00)
amp 7q21 2 465 (83%) 95 0.000402
(0.223)
1.21e-05
(0.00675)
0.565
(1.00)
0.507
(1.00)
0.106
(1.00)
0.148
(1.00)
0.036
(1.00)
0.0439
(1.00)
del 10p15 3 454 (81%) 106 2.81e-06
(0.00157)
1.49e-08
(8.43e-06)
0.185
(1.00)
0.523
(1.00)
0.00507
(1.00)
0.73
(1.00)
0.147
(1.00)
0.278
(1.00)
del 10p13 456 (81%) 104 1.99e-06
(0.00112)
7.92e-08
(4.48e-05)
0.0756
(1.00)
0.991
(1.00)
0.00384
(1.00)
0.817
(1.00)
0.119
(1.00)
0.27
(1.00)
del 10p11 23 461 (82%) 99 8.88e-08
(5.01e-05)
3.16e-10
(1.79e-07)
0.175
(1.00)
0.178
(1.00)
0.00214
(1.00)
0.812
(1.00)
0.136
(1.00)
0.251
(1.00)
del 10q23 31 497 (89%) 63 1.42e-05
(0.00788)
1.58e-07
(8.88e-05)
0.785
(1.00)
0.0823
(1.00)
0.00518
(1.00)
1
(1.00)
0.299
(1.00)
0.639
(1.00)
del 9p21 3 409 (73%) 151 0.0203
(1.00)
4.81e-05
(0.0267)
0.559
(1.00)
0.126
(1.00)
0.597
(1.00)
0.357
(1.00)
0.642
(1.00)
0.745
(1.00)
del 10q26 3 498 (89%) 62 0.000945
(0.522)
6.64e-06
(0.0037)
0.68
(1.00)
0.0838
(1.00)
0.0139
(1.00)
1
(1.00)
0.0833
(1.00)
0.636
(1.00)
amp 1p36 21 91 (16%) 469 0.064
(1.00)
0.309
(1.00)
0.482
(1.00)
0.189
(1.00)
0.0706
(1.00)
0.902
(1.00)
0.162
(1.00)
0.404
(1.00)
amp 1q32 1 155 (28%) 405 0.451
(1.00)
0.168
(1.00)
1
(1.00)
0.3
(1.00)
1
(1.00)
0.84
(1.00)
0.864
(1.00)
0.526
(1.00)
amp 1q44 97 (17%) 463 0.347
(1.00)
0.868
(1.00)
0.304
(1.00)
0.417
(1.00)
0.153
(1.00)
0.55
(1.00)
0.771
(1.00)
0.427
(1.00)
amp 2p24 3 48 (9%) 512 0.255
(1.00)
0.34
(1.00)
0.356
(1.00)
0.924
(1.00)
1
(1.00)
0.748
(1.00)
0.51
(1.00)
0.612
(1.00)
amp 3q26 33 108 (19%) 452 0.283
(1.00)
0.0395
(1.00)
0.661
(1.00)
0.714
(1.00)
0.00467
(1.00)
0.909
(1.00)
0.261
(1.00)
0.701
(1.00)
amp 4p16 3 48 (9%) 512 0.851
(1.00)
0.806
(1.00)
0.356
(1.00)
0.373
(1.00)
1
(1.00)
0.748
(1.00)
0.691
(1.00)
1
(1.00)
amp 4q12 105 (19%) 455 0.349
(1.00)
0.163
(1.00)
0.376
(1.00)
0.823
(1.00)
0.332
(1.00)
0.296
(1.00)
0.684
(1.00)
1
(1.00)
amp 7q31 2 458 (82%) 102 0.00652
(1.00)
0.00225
(1.00)
0.433
(1.00)
0.861
(1.00)
0.216
(1.00)
0.0595
(1.00)
0.047
(1.00)
0.055
(1.00)
amp 8q24 21 70 (12%) 490 0.257
(1.00)
0.4
(1.00)
0.516
(1.00)
0.94
(1.00)
1
(1.00)
0.681
(1.00)
0.0597
(1.00)
1
(1.00)
amp 11p13 29 (5%) 531 0.805
(1.00)
0.374
(1.00)
0.847
(1.00)
0.59
(1.00)
0.844
(1.00)
1
(1.00)
0.537
(1.00)
0.51
(1.00)
amp 12p13 32 82 (15%) 478 0.86
(1.00)
0.184
(1.00)
1
(1.00)
0.789
(1.00)
0.74
(1.00)
0.521
(1.00)
0.55
(1.00)
0.685
(1.00)
amp 12q14 1 131 (23%) 429 0.326
(1.00)
0.561
(1.00)
0.359
(1.00)
0.85
(1.00)
0.487
(1.00)
0.749
(1.00)
0.753
(1.00)
0.31
(1.00)
amp 12q15 91 (16%) 469 0.782
(1.00)
0.481
(1.00)
0.413
(1.00)
0.902
(1.00)
0.874
(1.00)
0.462
(1.00)
0.649
(1.00)
0.23
(1.00)
amp 13q34 32 (6%) 528 0.826
(1.00)
0.653
(1.00)
0.36
(1.00)
0.541
(1.00)
0.461
(1.00)
0.701
(1.00)
0.771
(1.00)
1
(1.00)
amp 13q34 29 (5%) 531 0.694
(1.00)
0.536
(1.00)
0.698
(1.00)
0.395
(1.00)
0.848
(1.00)
0.687
(1.00)
0.623
(1.00)
1
(1.00)
amp 14q32 33 36 (6%) 524 0.475
(1.00)
0.0061
(1.00)
0.486
(1.00)
0.311
(1.00)
0.228
(1.00)
1
(1.00)
1
(1.00)
1
(1.00)
amp 17p13 2 50 (9%) 510 0.583
(1.00)
0.643
(1.00)
0.175
(1.00)
0.947
(1.00)
0.344
(1.00)
0.526
(1.00)
0.683
(1.00)
1
(1.00)
amp 17q25 1 81 (14%) 479 0.0231
(1.00)
0.00884
(1.00)
0.176
(1.00)
0.452
(1.00)
0.859
(1.00)
0.606
(1.00)
0.188
(1.00)
0.689
(1.00)
amp 19p13 3 236 (42%) 324 0.24
(1.00)
0.61
(1.00)
1
(1.00)
0.13
(1.00)
0.527
(1.00)
0.927
(1.00)
0.418
(1.00)
0.572
(1.00)
amp 19p13 2 241 (43%) 319 0.161
(1.00)
0.948
(1.00)
0.931
(1.00)
0.471
(1.00)
0.472
(1.00)
1
(1.00)
0.724
(1.00)
0.77
(1.00)
amp 19q12 209 (37%) 351 0.411
(1.00)
0.681
(1.00)
0.655
(1.00)
0.999
(1.00)
0.573
(1.00)
0.851
(1.00)
0.756
(1.00)
0.385
(1.00)
amp 21q21 1 68 (12%) 492 0.637
(1.00)
0.016
(1.00)
1
(1.00)
0.373
(1.00)
0.0637
(1.00)
0.404
(1.00)
0.104
(1.00)
0.378
(1.00)
del 1p36 32 96 (17%) 464 0.927
(1.00)
0.68
(1.00)
0.029
(1.00)
0.652
(1.00)
0.43
(1.00)
1
(1.00)
0.143
(1.00)
0.701
(1.00)
del 1p36 23 130 (23%) 430 0.534
(1.00)
0.224
(1.00)
0.00771
(1.00)
0.0989
(1.00)
0.197
(1.00)
0.391
(1.00)
0.158
(1.00)
0.312
(1.00)
del 1p32 3 60 (11%) 500 0.591
(1.00)
0.0637
(1.00)
0.126
(1.00)
0.628
(1.00)
1
(1.00)
0.106
(1.00)
0.304
(1.00)
1
(1.00)
del 1p22 1 47 (8%) 513 0.515
(1.00)
0.39
(1.00)
1
(1.00)
0.357
(1.00)
0.113
(1.00)
0.624
(1.00)
0.747
(1.00)
1
(1.00)
del 1q42 11 48 (9%) 512 0.111
(1.00)
0.402
(1.00)
0.878
(1.00)
0.0444
(1.00)
0.785
(1.00)
0.144
(1.00)
0.358
(1.00)
0.249
(1.00)
del 1q44 34 (6%) 526 0.525
(1.00)
0.344
(1.00)
1
(1.00)
0.305
(1.00)
0.415
(1.00)
0.705
(1.00)
0.649
(1.00)
0.482
(1.00)
del 2q22 1 45 (8%) 515 0.334
(1.00)
0.071
(1.00)
0.34
(1.00)
0.586
(1.00)
0.152
(1.00)
0.0665
(1.00)
0.367
(1.00)
0.612
(1.00)
del 2q37 1 54 (10%) 506 0.952
(1.00)
0.707
(1.00)
0.187
(1.00)
0.64
(1.00)
0.808
(1.00)
0.282
(1.00)
0.618
(1.00)
1
(1.00)
del 3p21 1 52 (9%) 508 0.0184
(1.00)
0.0219
(1.00)
0.882
(1.00)
0.792
(1.00)
0.24
(1.00)
0.0427
(1.00)
0.446
(1.00)
0.338
(1.00)
del 3q13 31 58 (10%) 502 0.62
(1.00)
0.17
(1.00)
0.395
(1.00)
0.245
(1.00)
0.499
(1.00)
0.372
(1.00)
0.196
(1.00)
0.377
(1.00)
del 3q22 1 58 (10%) 502 0.623
(1.00)
0.354
(1.00)
1
(1.00)
0.447
(1.00)
0.5
(1.00)
0.766
(1.00)
0.231
(1.00)
0.377
(1.00)
del 3q29 65 (12%) 495 0.319
(1.00)
0.525
(1.00)
1
(1.00)
0.331
(1.00)
0.575
(1.00)
0.325
(1.00)
0.93
(1.00)
1
(1.00)
del 4p16 3 76 (14%) 484 0.454
(1.00)
0.0775
(1.00)
0.256
(1.00)
0.365
(1.00)
0.524
(1.00)
0.113
(1.00)
0.526
(1.00)
0.662
(1.00)
del 4q34 3 89 (16%) 471 0.189
(1.00)
0.173
(1.00)
0.0339
(1.00)
0.581
(1.00)
0.936
(1.00)
0.137
(1.00)
0.248
(1.00)
1
(1.00)
del 5q35 3 52 (9%) 508 0.0364
(1.00)
0.228
(1.00)
1
(1.00)
0.94
(1.00)
1
(1.00)
0.348
(1.00)
0.84
(1.00)
0.0858
(1.00)
del 6q22 31 156 (28%) 404 0.0545
(1.00)
0.245
(1.00)
0.101
(1.00)
0.487
(1.00)
0.5
(1.00)
1
(1.00)
0.309
(1.00)
0.193
(1.00)
del 6q26 177 (32%) 383 0.102
(1.00)
0.959
(1.00)
0.264
(1.00)
0.919
(1.00)
0.229
(1.00)
0.846
(1.00)
0.622
(1.00)
0.353
(1.00)
del 8p23 2 65 (12%) 495 0.194
(1.00)
0.0401
(1.00)
0.348
(1.00)
0.246
(1.00)
0.836
(1.00)
0.674
(1.00)
0.0176
(1.00)
0.376
(1.00)
del 9q34 2 76 (14%) 484 0.952
(1.00)
0.995
(1.00)
1
(1.00)
0.709
(1.00)
0.101
(1.00)
0.691
(1.00)
0.451
(1.00)
0.23
(1.00)
del 11p15 5 127 (23%) 433 0.0197
(1.00)
0.00568
(1.00)
0.216
(1.00)
0.17
(1.00)
0.474
(1.00)
0.829
(1.00)
1
(1.00)
1
(1.00)
del 11p11 2 103 (18%) 457 0.0732
(1.00)
0.693
(1.00)
0.221
(1.00)
0.549
(1.00)
0.245
(1.00)
0.815
(1.00)
0.713
(1.00)
1
(1.00)
del 11q14 1 95 (17%) 465 0.945
(1.00)
0.627
(1.00)
0.3
(1.00)
0.871
(1.00)
0.371
(1.00)
0.116
(1.00)
1
(1.00)
0.7
(1.00)
del 12p13 1 71 (13%) 489 0.1
(1.00)
0.962
(1.00)
0.437
(1.00)
0.412
(1.00)
0.602
(1.00)
0.413
(1.00)
0.276
(1.00)
1
(1.00)
del 12q12 74 (13%) 486 0.443
(1.00)
0.664
(1.00)
0.8
(1.00)
0.989
(1.00)
0.853
(1.00)
0.505
(1.00)
0.433
(1.00)
0.655
(1.00)
del 12q15 76 (14%) 484 0.638
(1.00)
0.601
(1.00)
0.45
(1.00)
0.353
(1.00)
0.922
(1.00)
0.354
(1.00)
0.215
(1.00)
0.205
(1.00)
del 13q14 2 234 (42%) 326 0.983
(1.00)
0.681
(1.00)
0.792
(1.00)
0.836
(1.00)
0.234
(1.00)
0.646
(1.00)
0.275
(1.00)
1
(1.00)
del 14q13 1 174 (31%) 386 0.628
(1.00)
0.553
(1.00)
0.113
(1.00)
0.544
(1.00)
0.808
(1.00)
0.695
(1.00)
0.112
(1.00)
0.117
(1.00)
del 14q24 2 170 (30%) 390 0.717
(1.00)
0.525
(1.00)
0.259
(1.00)
0.852
(1.00)
0.647
(1.00)
0.622
(1.00)
0.379
(1.00)
1
(1.00)
del 15q14 147 (26%) 413 0.311
(1.00)
0.0344
(1.00)
0.768
(1.00)
0.956
(1.00)
0.79
(1.00)
0.41
(1.00)
0.168
(1.00)
0.324
(1.00)
del 16p12 2 92 (16%) 468 0.0581
(1.00)
0.235
(1.00)
0.352
(1.00)
0.709
(1.00)
0.51
(1.00)
0.392
(1.00)
0.464
(1.00)
1
(1.00)
del 16q23 3 95 (17%) 465 0.0285
(1.00)
0.78
(1.00)
0.565
(1.00)
0.0836
(1.00)
0.877
(1.00)
0.011
(1.00)
0.161
(1.00)
0.701
(1.00)
del 17p13 2 82 (15%) 478 0.73
(1.00)
0.457
(1.00)
0.271
(1.00)
0.405
(1.00)
0.74
(1.00)
0.799
(1.00)
1
(1.00)
0.702
(1.00)
del 17p13 1 92 (16%) 468 0.449
(1.00)
0.132
(1.00)
0.0796
(1.00)
0.996
(1.00)
0.583
(1.00)
0.178
(1.00)
0.948
(1.00)
1
(1.00)
del 17q11 2 68 (12%) 492 0.264
(1.00)
0.538
(1.00)
0.895
(1.00)
0.381
(1.00)
0.916
(1.00)
0.0948
(1.00)
0.815
(1.00)
1
(1.00)
del 18q22 3 80 (14%) 480 0.571
(1.00)
0.497
(1.00)
0.805
(1.00)
0.114
(1.00)
0.859
(1.00)
0.698
(1.00)
0.405
(1.00)
0.398
(1.00)
del 19q13 41 98 (18%) 462 0.0179
(1.00)
0.355
(1.00)
0.91
(1.00)
0.693
(1.00)
0.727
(1.00)
1
(1.00)
0.378
(1.00)
1
(1.00)
del 21q22 11 46 (8%) 514 0.882
(1.00)
0.294
(1.00)
0.756
(1.00)
0.188
(1.00)
0.689
(1.00)
0.321
(1.00)
0.454
(1.00)
0.081
(1.00)
del 22q13 32 210 (38%) 350 0.97
(1.00)
0.187
(1.00)
0.789
(1.00)
0.481
(1.00)
0.623
(1.00)
0.574
(1.00)
0.362
(1.00)
1
(1.00)
del xp22 2 115 (21%) 445 0.297
(1.00)
0.655
(1.00)
0.831
(1.00)
0.285
(1.00)
0.946
(1.00)
1
(1.00)
0.588
(1.00)
0.474
(1.00)
del xq23 106 (19%) 454 0.204
(1.00)
0.437
(1.00)
0.659
(1.00)
0.247
(1.00)
0.788
(1.00)
0.419
(1.00)
0.341
(1.00)
0.478
(1.00)
'amp_7p11.2' versus 'Time to Death'

P value = 4.09e-07 (logrank test), Q value = 0.00023

Table S1.  Gene #8: 'amp_7p11.2' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 560 462 0.1 - 127.6 (10.1)
AMP PEAK 8(7P11.2) MUTATED 492 414 0.1 - 127.6 (9.5)
AMP PEAK 8(7P11.2) WILD-TYPE 68 48 0.2 - 108.8 (15.1)

Figure S1.  Get High-res Image Gene #8: 'amp_7p11.2' versus Clinical Feature #1: 'Time to Death'

'amp_7p11.2' versus 'AGE'

P value = 6.33e-12 (Wilcoxon-test), Q value = 3.6e-09

Table S2.  Gene #8: 'amp_7p11.2' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 560 57.9 (14.5)
AMP PEAK 8(7P11.2) MUTATED 492 59.8 (12.5)
AMP PEAK 8(7P11.2) WILD-TYPE 68 43.6 (18.8)

Figure S2.  Get High-res Image Gene #8: 'amp_7p11.2' versus Clinical Feature #2: 'AGE'

'amp_7q11.21' versus 'Time to Death'

P value = 3.31e-05 (logrank test), Q value = 0.018

Table S3.  Gene #9: 'amp_7q11.21' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 560 462 0.1 - 127.6 (10.1)
AMP PEAK 9(7Q11.21) MUTATED 450 376 0.1 - 127.6 (9.4)
AMP PEAK 9(7Q11.21) WILD-TYPE 110 86 0.2 - 108.8 (13.8)

Figure S3.  Get High-res Image Gene #9: 'amp_7q11.21' versus Clinical Feature #1: 'Time to Death'

'amp_7q11.21' versus 'AGE'

P value = 3.29e-07 (Wilcoxon-test), Q value = 0.00018

Table S4.  Gene #9: 'amp_7q11.21' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 560 57.9 (14.5)
AMP PEAK 9(7Q11.21) MUTATED 450 59.9 (12.5)
AMP PEAK 9(7Q11.21) WILD-TYPE 110 49.5 (18.5)

Figure S4.  Get High-res Image Gene #9: 'amp_7q11.21' versus Clinical Feature #2: 'AGE'

'amp_7q21.2' versus 'Time to Death'

P value = 0.000402 (logrank test), Q value = 0.22

Table S5.  Gene #10: 'amp_7q21.2' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 560 462 0.1 - 127.6 (10.1)
AMP PEAK 10(7Q21.2) MUTATED 465 390 0.1 - 127.6 (9.7)
AMP PEAK 10(7Q21.2) WILD-TYPE 95 72 0.1 - 108.8 (12.4)

Figure S5.  Get High-res Image Gene #10: 'amp_7q21.2' versus Clinical Feature #1: 'Time to Death'

'amp_7q21.2' versus 'AGE'

P value = 1.21e-05 (Wilcoxon-test), Q value = 0.0068

Table S6.  Gene #10: 'amp_7q21.2' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 560 57.9 (14.5)
AMP PEAK 10(7Q21.2) MUTATED 465 59.5 (12.5)
AMP PEAK 10(7Q21.2) WILD-TYPE 95 49.7 (19.8)

Figure S6.  Get High-res Image Gene #10: 'amp_7q21.2' versus Clinical Feature #2: 'AGE'

'del_9p21.3' versus 'AGE'

P value = 4.81e-05 (Wilcoxon-test), Q value = 0.027

Table S7.  Gene #44: 'del_9p21.3' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 560 57.9 (14.5)
DEL PEAK 19(9P21.3) MUTATED 409 59.3 (13.7)
DEL PEAK 19(9P21.3) WILD-TYPE 151 54.0 (15.7)

Figure S7.  Get High-res Image Gene #44: 'del_9p21.3' versus Clinical Feature #2: 'AGE'

'del_10p15.3' versus 'Time to Death'

P value = 2.81e-06 (logrank test), Q value = 0.0016

Table S8.  Gene #46: 'del_10p15.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 560 462 0.1 - 127.6 (10.1)
DEL PEAK 21(10P15.3) MUTATED 454 383 0.1 - 92.7 (9.9)
DEL PEAK 21(10P15.3) WILD-TYPE 106 79 0.1 - 127.6 (11.7)

Figure S8.  Get High-res Image Gene #46: 'del_10p15.3' versus Clinical Feature #1: 'Time to Death'

'del_10p15.3' versus 'AGE'

P value = 1.49e-08 (Wilcoxon-test), Q value = 8.4e-06

Table S9.  Gene #46: 'del_10p15.3' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 560 57.9 (14.5)
DEL PEAK 21(10P15.3) MUTATED 454 59.9 (12.5)
DEL PEAK 21(10P15.3) WILD-TYPE 106 49.0 (18.5)

Figure S9.  Get High-res Image Gene #46: 'del_10p15.3' versus Clinical Feature #2: 'AGE'

'del_10p13' versus 'Time to Death'

P value = 1.99e-06 (logrank test), Q value = 0.0011

Table S10.  Gene #47: 'del_10p13' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 560 462 0.1 - 127.6 (10.1)
DEL PEAK 22(10P13) MUTATED 456 384 0.1 - 92.7 (9.9)
DEL PEAK 22(10P13) WILD-TYPE 104 78 0.1 - 127.6 (11.5)

Figure S10.  Get High-res Image Gene #47: 'del_10p13' versus Clinical Feature #1: 'Time to Death'

'del_10p13' versus 'AGE'

P value = 7.92e-08 (Wilcoxon-test), Q value = 4.5e-05

Table S11.  Gene #47: 'del_10p13' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 560 57.9 (14.5)
DEL PEAK 22(10P13) MUTATED 456 59.8 (12.4)
DEL PEAK 22(10P13) WILD-TYPE 104 49.2 (19.0)

Figure S11.  Get High-res Image Gene #47: 'del_10p13' versus Clinical Feature #2: 'AGE'

'del_10p11.23' versus 'Time to Death'

P value = 8.88e-08 (logrank test), Q value = 5e-05

Table S12.  Gene #48: 'del_10p11.23' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 560 462 0.1 - 127.6 (10.1)
DEL PEAK 23(10P11.23) MUTATED 461 388 0.1 - 92.7 (9.7)
DEL PEAK 23(10P11.23) WILD-TYPE 99 74 0.1 - 127.6 (12.9)

Figure S12.  Get High-res Image Gene #48: 'del_10p11.23' versus Clinical Feature #1: 'Time to Death'

'del_10p11.23' versus 'AGE'

P value = 3.16e-10 (Wilcoxon-test), Q value = 1.8e-07

Table S13.  Gene #48: 'del_10p11.23' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 560 57.9 (14.5)
DEL PEAK 23(10P11.23) MUTATED 461 60.0 (12.3)
DEL PEAK 23(10P11.23) WILD-TYPE 99 47.7 (18.8)

Figure S13.  Get High-res Image Gene #48: 'del_10p11.23' versus Clinical Feature #2: 'AGE'

'del_10q23.31' versus 'Time to Death'

P value = 1.42e-05 (logrank test), Q value = 0.0079

Table S14.  Gene #49: 'del_10q23.31' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 560 462 0.1 - 127.6 (10.1)
DEL PEAK 24(10Q23.31) MUTATED 497 416 0.1 - 127.6 (9.9)
DEL PEAK 24(10Q23.31) WILD-TYPE 63 46 0.2 - 108.8 (12.7)

Figure S14.  Get High-res Image Gene #49: 'del_10q23.31' versus Clinical Feature #1: 'Time to Death'

'del_10q23.31' versus 'AGE'

P value = 1.58e-07 (Wilcoxon-test), Q value = 8.9e-05

Table S15.  Gene #49: 'del_10q23.31' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 560 57.9 (14.5)
DEL PEAK 24(10Q23.31) MUTATED 497 59.2 (13.3)
DEL PEAK 24(10Q23.31) WILD-TYPE 63 47.2 (18.6)

Figure S15.  Get High-res Image Gene #49: 'del_10q23.31' versus Clinical Feature #2: 'AGE'

'del_10q26.3' versus 'AGE'

P value = 6.64e-06 (Wilcoxon-test), Q value = 0.0037

Table S16.  Gene #50: 'del_10q26.3' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 560 57.9 (14.5)
DEL PEAK 25(10Q26.3) MUTATED 498 59.1 (13.4)
DEL PEAK 25(10Q26.3) WILD-TYPE 62 48.3 (18.7)

Figure S16.  Get High-res Image Gene #50: 'del_10q26.3' versus Clinical Feature #2: 'AGE'

Methods & Data
Input
  • Copy number data file = transformed.cor.cli.txt

  • Clinical data file = GBM-TP.merged_data.txt

  • Number of patients = 560

  • Number of significantly focal cnvs = 71

  • Number of selected clinical features = 8

  • Exclude genes that fewer than K tumors have mutations, K = 3

Survival analysis

For survival clinical features, the Kaplan-Meier survival curves of tumors with and without gene mutations were plotted and the statistical significance P values were estimated by logrank test (Bland and Altman 2004) using the 'survdiff' function in R

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Bland and Altman, Statistics notes: The logrank test, BMJ 328(7447):1073 (2004)
[2] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[3] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)